I was thinking the other way around; the building was built on an outcropping and the lower windows holes carved into the cliff face to connect a natural cave within to the outside.
I understand what you mean though, and I did notice the face's upper edge was high while roofing the secondary section, but I'll be keeping the same general design regardless of this.
I didn't go/am not going for realism on this environment build; there's a bar off to the side (not pictured) which goes completely against the concept of what is possible and what is impossible/impractical.
and yes, its not done. The terrain on the outside isn't done, as well as touchups on the terrain moulding and grass on the cliff ledges